With good JHPs, both are so close that it really won't matter. First, pick a platform that feels and points the most naturally for you. Then, look at the available calibers and make a selection based on your own priorities. For me, given the choice, I'd stick with 9mm. Lower ammo costs, quicker follow up shots (given the same platform) and often the bonus of an extra round or three.
In the end though, my only semi automatic is a .45 ACP. Go figure.
(I shoot 1911s better than any other auto I've tried).